Not going to get into what's best, and while somewhat a function of cost, Galfer superbike wave rotors (and I have these on another bike) , Braketech ductile iron (I've owned these also), Braking, etc. plus some trick pads - are all pretty spendy. Application matters. A lot.
Sure, you can go nuts. Why not some ceramic rotors? Better throw a pair of those new Brembo monoblocks with the lithium alloy. Might as well fit up some Ohlins twin-tube SBK forks while at it. CF wheels - an absolute must! And lastly, a forged body Brembo master cylinder with the fold-away adjustable-from-the-left lever.
Not racing? Occasional trackday? Bike nighter (don't forget the Ti bolts!)? Street only? Factory stuff works great. Not merely good - but great. For the bike's intended uses, I've never experienced better functioning brakes out of the box. If the rules allowed, would I go racing for money with what the SD comes with? Probably not.
And I can stand the SD on its nose with two fingers with little effort - bone stock. I like both their progression and feel. I don't like super-grabby brakes around town (any 916/996 owners here?), or large-piston diameter master cylinders. I like feeding-in my brakes. And I like doing so as late as possible. So much shit on the road, can't afford anything too abrupt. Stock lever too. Longer = more leverage = more control resolution over lever distance moved. In fairness, I have huge hands, and Popeye forearms.
As I usually run my SuperDuke only at the less-fast courses in the region (and we have a couple of very fast courses here), I have never (!) experienced any fade. None. Not all day. Again - stock pads. And I know damn well I brake harder than most riders - one of the most effective ways to pass on the track. And I ain't no scrawny chicken-legged kid either - my brakes get worked.
As for "feel", a fairly subjective matter (although, "wooden" is pretty much "wooden" - we all know what that is). Have I used brakes that required less effort? You bet. And on one of those bikes with a one-finger-stoppie low-effort superbike setup, I've broken ribs stuffing the front end harder than there was traction for. What that setup lacked for me - was the ability to feed in braking as I like. Not making excuses, as going down was entirely my doing - but the setup just wasn't for me. Not for the average trail-brake-to-the-apex guy really (except maybe those that get paid to ride - where there would be more effective progression due to higher velocities).
Point: Can't argue with what some people clearly prefer in terms of performance, feel, progression, and whatever other criteria is important to them. They can justify their decisions with all sorts of test data and claims. Does the street rider benefit from off-the-shelf race technology? Maybe. I for one find the OEM setup excellent. Its all legitimate.
What matters beyond these subjective elements? Consistency. Knowing (without thinking) how your braking system is going to perform for a given condition, and that it does so the same every time - is the key to rider confidence. And my SuperDuke's brakes accomplish this for me perfectly, everywhere I use the bike, all the time. For others' setups, the right combination of pads, rotors, levers, master cylinders, calipers, and even wheels suits them better.
All good. But suggesting to a guy with what appears to be a fuckedup rotor, who clearly has yet to experience his SuperDuke brakes as they should function - to spend at least $500 (USD) to sort out his problems is a bit much IMO.